The structure of the dusty crystal is studied by Langevin molecular dynamics simulation when the influence of ion flow is taken into account. The “Yukawa/point-wake” model is used to describe the particle-particle interaction and particle-wake interaction in the dust system. The particles arrange themselves compactly and orderly in the horizontal direction and present a highly ordered structure under some conditions. The formed dusty crystal is quasi two-dimensional but presents a “bowl” shaped structure. The results are helpful in understanding the structure of dusty crystal in the presence of ion flow in the dusty plasma system.